30juni 2018. Added new version which does analysis from bcf/vcf and outputs all nine jacquards
This page refers to the new v2 of NgsRelate which coestimates relatedness and inbreeding. For the old version please use this link: http://www.popgen.dk/software/index.php?title=NgsRelate&oldid=694
This page contains information about the program called NgsRelate, which can be used to infer relatedness, inbreeding coefficients and many other summary statistics for pairs of individuals from low coverage Next Generation Sequencing (NGS) data by using genotype likelihoods instead of called genotypes. To be able to infer the relatedness you will need to know the population allele frequencies and have genotype likelihoods. This can be obtained e.g. using the program ANGSD as shown in example 1 below. For more information about ANGSD see here: http://popgen.dk/angsd/index.php/Quick_Start. As of version 2, VCF/BCF files can also be parsed.
$ ./ngsRelate
Usage main analyses: ./ngsrelate [options]
Options:
-f <filename> Name of file with frequencies
-O <filename> Output filename
-L <INT> Number of genomic sites. Must be provided if -f (allele frequency file) is NOT provided
-m <INTEGER> model 0=normalEM 1=acceleratedEM
-i <UINTEGER> Maximum number of EM iterations
-t <FLOAT> Tolerance for breaking EM
-r <FLOAT> Seed for rand
-R <chr:from-to> Region for analysis (only for bcf)
-g gfile Name of genotypellh file
-p <INT> threads (default 4)
-c <INT> Should call genotypes instead?
-s <INT> Should you swich the freq with 1-freq?
-F <INT> Estimate inbreeding instead of estimating the nine jacquard coefficients
-o <INT> estimating the 3 jacquard coefficient, assumming no inbreeding
-v <INT> Verbose. print like per iteration
-e <FLOAT> Errorrates when calling genotypes?
-a <INT> First individual used for analysis? (zero offset)
-b <INT> Second individual used for analysis? (zero offset)
-B <INT> Number of bootstrap replicates for (only for single pairs)
-N <INT> How many times to start each pair with random seed?
-n <INT> Number of samples in glf.gz
-l <INT> minMaf or 1-Maf filter
-z <INT> Name of file with IDs (optional)
-T <STRING> For -h vcf use PL (default) or GT tag
-A <STRING> For -h vcf use allele frequency TAG e.g. AFngsrelate (default)
-P <filename> plink name of the binary plink file (excluding the .bed)
Or
./ngsrelate extract_freq_bim pos.glf.gz plink.bim plink.freq
Or
./ngsrelate extract_freq .mafs.gz .pos.glf.gz [-rmTrans]
Or
./ngsrelate -h my.bcf [DEVELOPMENT ONLY]
On a linux or mac system with curl and g++ installed NgsRelate can be downloaded and installed as follows:
git clone --recursive https://github.com/SAMtools/htslib
git clone https://github.com/ANGSD/ngsRelate
cd htslib/;make -j2;cd ../ngsRelate;make HTSSRC=../htslib/Below is an example of how NgsRelate can be used to coestimate relatedness and inbreeding from NGS data.
Assume we have file (filelist) containing paths to 100 BAM/CRAM files; one line per BAM/CRAM file. Then we can use ANGSD to estimate allele frequencies and calculate genotype likelihoods while doing SNP calling and in the end produce the the two input files needed for the NgsRelate program as follows:
### First we generate a file with allele frequencies (angsdput.mafs.gz) and a file with genotype likelihoods (angsdput.glf.gz).
./angsd -b filelist -gl 2 -domajorminor 1 -snp_pval 1e-6 -domaf 1 -minmaf 0.05 -doGlf 3
### Then we extract the frequency column from the allele frequency file and remove the header (to make it in the format NgsRelate needs)
zcat angsdput.mafs.gz | cut -f5 |sed 1d >freq
### run NgsRelate
./ngsrelate -g angsdput.glf.gz -n 100 -f freq -O newresThe output should be a file called newres that contains the output for all pairs between six individuals.
As of version 2, NgsRelate can parse BCF/VCF files using htslib with the following command:
./ngsrelate -h my.VCF.gz -O vcf.resBy default, NgsRelate will estimate the allele frequencies using the individuals provided in the VCF files. Allele frequencies from the INFO field can used be used instead using -A TAG. The TAG usually take the form of AF or AF1 but can be set to anything. By default the PL data (Phred-scaled likelihoods for genotypes) is parsed, however, the called genotypes can also be used instead with the -T GT option.
If called genotypes are being used, the software requires an additional argument (-c 1). If using -c 2, ngsRelate calls genotypes assuming hardy-weinberg.
NgsRelate takes two files as input: a file with genotype likelihoods (-g) and a file with population allele frequencies (-f) for the sites there are genotype likelihoods for.
The genotype likelihood file needs to contain a line for each site with 3 values for each individual (one log transformed genotype likelihood for each of the 3 possible genotypes encoded as 'double's) and it needs to be in binary format and gz compressed.
The frequency file needs to contain a line per site with the allele frequency of the site in it.
NgsRelate also calculates a few summary statistics based on the 2dsfs instead of known population allele frequencies. Even if the population allele frequencies are not available, these summary statistics can still be estimated with NgsRelate by providing it with the number of sites (-L) instead of the allele frequency file (-f).
NgsRelate takes a standard VCF file generated with e.g. bcftools. By default, NgsRelate will estimate the allele frequencies using the individuals provided in the VCF files. As shown in example 2, external allele frequencies can be provided with -f. These frequencies will overwrite the ones estimated from the VCF file.
a b nSites J9 J8 J7 J6 J5 J4 J3 J2 J1 rab Fa Fb theta inbred_relatedness_1_2 inbred_relatedness_2_1 fraternity identity zygosity 2of3IDB FDiff loglh nIter coverage 2dsfs R0 R1 KING 2dsfs_loglike 2dsfsf_niter
0 1 99927 0.384487 0.360978 0.001416 0.178610 0.071681 0.000617 0.002172 0.000034 0.000005 0.237300 0.002828 0.250330 0.127884 0.001091 0.035846 0.001451 0.000005 0.001456 0.345411 -0.088997 -341223.335664 103 0.999270 0.154920,0.087526,0.038724,0.143087,0.155155,0.139345,0.038473,0.087632,0.155138 0.497548 0.290124 0.000991 -356967.175857 7The first two columns contain indices of the two individuals used for the analysis. The third column is the number of genomic sites considered. The following nine columns are the maximum likelihood (ML) estimates of the nine jacquard coefficients, where K0==J9; K1==J8; K2==J7 in absence of inbreeding. Based on these Jacquard coefficients, NgsRelate calculates 11 summary statistics:
- rab is the pairwise relatedness
(J1+J7+0.75*(J3+J5)+.5*J8)Hedrick et al - Fa is the inbreeding coefficient of individual a
J1+J2+J3+J4Jacquard - Fb is the inbreeding coefficient of individual b
J1+J2+J5+J6Jacquard - theta is the coefficient of kinship
J1 + 0.5*(J3+J5+J7) + 0.25*J8)Jacquard - inbred_relatedness_1_2
J1+0.5*J3Ackerman et al - inbred_relatedness_2_1
J1+0.5*J5Ackerman et al - fraternity
J2+J7Ackerman et al - identity
J1Ackerman et al - zygosity
J1+J2+J7Ackerman et al - Two-out-of-three IBD
J1+J2+J3+J5+J7+0.5*(J4+J6+J8)Miklos csuros - Inbreeding difference
0.5*(J4-J6)Miklos csuros - the log-likelihood of the ML estimate.
- number of EM iterations. If a
-1is displayed. A boundary estimate had a higher likelihood. - If differs from
-1, a boundary estimate had a higher likelihood. Reported loglikelihood should be highly similar to the corresponding value reported inloglh - fraction of sites used for the ML estimate
The remaining columns relate to statistics based on a 2D-SFS.
- 2dsfs estimates using the same methodology as implemented in realSFS, see ANGSD
- R0 Waples et al
- R1 Waples et al
- KING Waples et al
- the log-likelihood of the 2dsfs estimate.
- number of iterations for 2dsfs estimate
You can also input a file with the IDs of the individuals (on ID per line), using the -z option, in the same order as in the file filelist used to make the genotype likelihoods or the VCF file. If you do the output will also contain these IDs as column 3 and 4.
Note that in some cases nIter is -1. This indicates that values on the boundary of the parameter space had a higher likelihood than the values achieved using the EM-algorithm (ML methods sometimes have trouble finding the ML estimate when it is on the boundary of the parameter space, and we therefore test the boundary values explicitly and output these if these have the highest likelihood).
To get help and a list of all options simply type
./ngsrelateNote that for the new version of ngsRelate it is not necessary to flip the allele frequencies if the input allele frequencies are for the minor allele.
To run the old version (V1) that assumes both individuals to be out-bred, just add -o 1 to your command. This will force Jacqaurd coefficient 1-6 (the coefficients related to inbreeding) to zero.
./ngsrelate -o 1To only estimate inbreeding, use the following command
./ngsrelate -F 1- Method (v1) is published here: http://bioinformatics.oxfordjournals.org/content/early/2015/08/29/bioinformatics.btv509.abstract
- Method (v2) is published here: https://academic.oup.com/gigascience/article/8/5/giz034/5481763
[email protected], [email protected], and [email protected]
bcftools call -v -m test.bcf -Ob >small.bcf
bcftools view small.bcf -Oz -o small.vcf.gz -m2 -M2 -v snps
plink --vcf small.vcf.gz --make-bed --out small
bgzip small.bed
md5sum small.* >small.md5a <- file("test.glf", "rb")
nobs <- 1e8 # large number 3*N*Nsites
N <- 6 # number of individuals
mat <- matrix(readBin(a, "double", nobs ), byrow=T, ncol=3*N)
con <- file("outfile.glf", "wb")
writeBin(c(t(mat)), con=con)
close(con)
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